Amber Archive Nov 2009: by messages with attachments

[AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Mon Nov 02 2009 - 01:17:19 PST)
1. 2796 (33627 bytes)
2. 2796 (766 bytes)
[AMBER] amber 10 test failures... peker milas (Mon Nov 02 2009 - 06:18:29 PST)
1. TEST_FAILURES.diff (57608 bytes)
Re: [AMBER] Is it taking too much time Nicolas Sapay (Tue Nov 03 2009 - 00:57:55 PST)
1. nicolas_sapay.vcf (391 bytes)
[AMBER] error in reading namelist cntrl Giuseppe De Marco (Tue Nov 03 2009 - 11:44:01 PST)
1. rem.out.000 (2655 bytes)
[AMBER] Antechamber and Parmchk problems cyk5056 (Tue Nov 03 2009 - 18:22:38 PST)
1. TMS.pdb (5269 bytes)
2. TMS.prep (4555 bytes)
Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Wed Nov 04 2009 - 11:56:32 PST)
1. 15.gif (1237 bytes)
Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber zgong.hust (Wed Nov 04 2009 - 18:18:52 PST)
1. 1y26_a.pdb (123796 bytes)
2. CUA.mol2 (1179 bytes)
Re: [AMBER] HB for each snapshot Nicolas Sapay (Thu Nov 05 2009 - 00:30:51 PST)
1. nicolas_sapay.vcf (391 bytes)
[AMBER] unable to find mopac charges in mopac.out Richard Tseng (Fri Nov 06 2009 - 17:14:20 PST)
1. ps_jm3_deepview.pdb (4575 bytes)
[AMBER] sleap fastbld error Oliver Kuhn (Sat Nov 07 2009 - 12:39:29 PST)
1. lig.pdb (3969 bytes)
[AMBER] sleap fastbld error is not an error Oliver Kuhn (Sat Nov 07 2009 - 13:07:35 PST)
1. lig.pdb (3969 bytes)
[AMBER] Task is running on supercomputer without any output Andrew Voronkov (Mon Nov 09 2009 - 04:39:36 PST)
1. 15750 (717 bytes)
Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng (Mon Nov 09 2009 - 08:39:51 PST)
1. mopac.out (7819 bytes)
RE: [AMBER] PCA analysis with ptraj hannes.loeffler.stfc.ac.uk (Tue Nov 10 2009 - 00:13:29 PST)
1. winmail.dat (0 bytes)
[AMBER] three trials to create topologies with sleap and tleap Oliver Kuhn (Tue Nov 10 2009 - 01:34:36 PST)
1. lig.pdb (3969 bytes)
2. rec.pdb (122796 bytes)
[AMBER] MMTSB tool set PDF kureeckal ramesh (Tue Nov 10 2009 - 06:02:39 PST)
1. MMTSB.pdf (786679 bytes)
[AMBER] enquiry regarding parameter file to be used bharat lakhani (Fri Nov 13 2009 - 05:35:30 PST)
1. DRUG0minvac.out (14317 bytes)
2. minvac.in (110 bytes)
[AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 07:56:04 PST)
1. analyse_hbond.ptraj (2586 bytes)
Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 08:19:04 PST)
1. analyse_hbond.ptraj (2586 bytes)
Re: [AMBER] Segmentation fault in antechamber albert albert (Tue Nov 17 2009 - 09:04:46 PST)
1. pdb3brp.ent.gz (67709 bytes)
Re: [AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 17:51:38 PST)
1. fzd8min_renum_SS.pdb (315243 bytes)
[AMBER] Can I get an average trajectory? cyk5056 (Tue Nov 17 2009 - 20:46:25 PST)
1. 15.gif (1237 bytes)
[AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure Yunjie Zhao (Thu Nov 19 2009 - 20:37:34 PST)
1. sam.pdb (2158 bytes)
[AMBER] rmsd Taufik Al-Sarraj (Fri Nov 20 2009 - 08:32:24 PST)
1. rmsd.jpg (91333 bytes)
[AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 07:51:00 PST)
1. analyse_hbond.ptraj (1708 bytes)
2. analyse_hbond.out (8143 bytes)
3. jsridhar.vcf (205 bytes)
Re: [AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 10:36:25 PST)
1. jsridhar.vcf (205 bytes)
[AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 08:32:41 PST)
1. analyse_hbond2.ptraj (522 bytes)
2. analyse_hbond2.out (20619 bytes)
3. jsridhar.vcf (205 bytes)
RE: [AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 09:52:47 PST)
1. jsridhar.vcf (205 bytes)
Re: [AMBER] i-APBS and apbs Rilei Yu (Wed Nov 25 2009 - 03:14:15 PST)
1. results.tar.gz (259686 bytes)
[AMBER] rings getting planar Jio M (Thu Nov 26 2009 - 01:33:09 PST)
1. Screenshot.png (37708 bytes)
Re: [AMBER] Re: MM_PBSA error Jagdeesh C (Fri Nov 27 2009 - 02:13:36 PST)
1. snapshot_com.all.out (69912 bytes)
2. binding_energy.log (14930 bytes)

Amber Archive Nov 2009 by messages with attachments